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## org.metaqtl.factory
Class TreeFactory

    java.lang.Object
      org.metaqtl.factory.TreeFactory

    public final class TreeFactory

extends java.lang.Object

A factory to deal with distance trees.

Constructor Summary
`TreeFactory()`

Method Summary
`static Tree` | `read_newick(java.io.Reader reader)`
`static Tree` | `read_newick(java.lang.String treeStr)`
`static Tree` | `read(java.io.Reader reader)`
`static Tree` | `read(java.lang.String str)`
`static void` | `write(Tree tree, java.io.OutputStream stream)` This method writes out the given tree `nodes` as an array of `TreeNode` on the given output stream stream.
`static void` | `write(Tree tree, java.io.PrintWriter writer)` This method writes out the given tree `nodes` as an array of `TreeNode` using the given writer writer.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

### TreeFactory

    public TreeFactory()

Method Detail

### write

    public static void write(Tree tree,
                             java.io.OutputStream stream)
                      throws java.io.IOException

  This method writes out the given tree `nodes` as an array of `TreeNode` on the given output stream stream. The user is responsible for closing the stream.

  Parameters:
    `nodes` - the tree
    `stream` - the output stream.
  Throws:
    `java.io.IOException`

### write

    public static void write(Tree tree,
                             java.io.PrintWriter writer)

  This method writes out the given tree `nodes` as an array of `TreeNode` using the given writer writer.

  Parameters:
    `nodes` - the tree
    `writer` - the writer.

### read_newick

    public static Tree read_newick(java.io.Reader reader)
                            throws java.io.IOException

  Parameters:
    `cur` -
    `root` -
    `reader` -
  Throws:
    `java.io.IOException`

### read_newick

    public static Tree read_newick(java.lang.String treeStr)
                            throws java.io.IOException

  Parameters:
    `treeStr` -
  Returns:
  Throws:
    `java.io.IOException`

### read

    public static Tree read(java.io.Reader reader)
                     throws java.io.IOException

  Parameters:
    `buffer` -
  Returns:
  Throws:
    `java.io.IOException`

### read

    public static Tree read(java.lang.String str)
                     throws java.io.IOException

  Throws:
    `java.io.IOException`

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